Thanks for your prompt reply, according to you for membrane protein protocols keep restrain only on protein but not on lipid and water, is there any possibility to move water inside pore of the membrane when keep restrain only on protein. Could you please tell me Thanks a lot in advance
On Sun, 29 Jun 2008 Justin A.Lemkul wrote : > > >minnale wrote: >> >> HI users, >> I have embedded protein in popc bilayer and ran the minimisation >> succesfully , before going equilibration I would like to confirm one thing >> that how to run the equilibration with on which system keep position >> restrain? >> >>1.we will keep position restrain on all the systems(-DPOSRES_PROTEIN, >>-DPOSRES_LIPID, -DPOSRES_WATER) at a time ? >> >>or 2. keep position resrain on each system at a time and >> 3.is it require to keep position restrain on water? >>Could you tell me clearly pls >>Thanks alot in advance >> >> > >If you "equilibrate" your system with every element of it restrained, I think >you will accomplish absolutely nothing. Typical procedures for membrane >proteins involve equilibrating with restraints on the protein only, allowing >the lipids to pack around the protein. >-Justin > >> >>HSBC >><http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/[EMAIL >> PROTECTED]/2204104_2196511/2199118/1?PARTNER=3&OAS_QUERY=null> >> >>------------------------------------------------------------------------ >> >>_______________________________________________ >>gmx-users mailing list gmx-users@gromacs.org >>http://www.gromacs.org/mailman/listinfo/gmx-users >>Please search the archive at http://www.gromacs.org/search before posting! >>Please don't post (un)subscribe requests to the list. Use the www interface >>or send it to [EMAIL PROTECTED] >>Can't post? Read http://www.gromacs.org/mailing_lists/users.php > >-- ======================================== > >Justin A. Lemkul >Graduate Research Assistant >Department of Biochemistry >Virginia Tech >Blacksburg, VA >jalemkul[at]vt.edu | (540) 231-9080 >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > >======================================== >
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